yeah, so far as i see it. it spits out the random number which corresponds to what symbols show, and the rest is calculation based on the winline and amounts bet on those winlines. computers can always do math accurately.
UNLESS as has been posited that the symbols are "all for show" and a numeric win (properly weighted based on the paytable/reel layout or not?) is selected and the software mistakenly/lazily displays an improper graphic when trying to represent that win amount. i still think it would have to check what the bet is on each line before it displays any symbols in order to make the output look acceptable, but there could be room for an unintentional winline appearing but overlooked by the game when the "meaningless" graphic is generated.
i suppose even in the first scenario there is a chance for error in the looking up of the winlines, but i don't think this is what you are talking about anyway. it sounds like you're asserting that all of the winlines were paid disproportionately, not a failure of any one winline to register.
sorry i can't be more help, but i really don't think it's possible, unless maybe they filled the viewable paytable out wrong. did you have the same win at a lower bet for the same absolute amount, or was it the first time you got that sort of win and it didn't correspond to what the paytable shows? that's the only other idea i can come up with.